Hello Peter,
Your last error is because HDS requires a fair amount of data to be present before the stream will work, and HDS is the default streamout method when Flash player is installed.
If you disable/remove the HDS output in the protocols section of the configuration page, that should resolve your problem as it will fall back to other streaming methods then.
Bad latency shouldn't be a problem, as long as you can sustain the bandwidth long-term.
If you cannot sustain the bandwidth for your stream, it's best to use a method that stays connected but drops frames when throughput goes down. Most RTMP push clients will do this for you automatically already, with the exception of FMLE which does not.
Lowering the timeouts altogether can be done by lowering the buffer size (eg: 10000 ms instead of the default of 50000 ms) and segment size (eg: 2000 ms instead of the default of 5000 ms) while lowering your source keyframe interval (a keyframe once every 1-2 seconds is usually a good value). Do note that this has a side effect of increasing the bandwidth usage slightly.
Hope that helps!
- Jaron